López started the stage 99 seconds ahead of Richie Porte (Trek-Segafredo), but that proved nowhere near enough as the Australian produced a brilliant time trial to place third on the stage.
The Colombian was caught and passed by both Pogačar and Roglič during the stage - ultimately placing 45th - some four minutes and 56 seconds down on Porte.
It means in the GC standings, López not only lost third place, but was also passed by Mikel Landa (Bahrain McLaren) and Enric Mas (Movistar) - plummeting to sixth overall in the process, 6:47 behind 2020 Tour de France champion Pogačar.
"It was a difficult day, a complicated day. I didn't feel good today, and that's how it went," López said, according to El Tiempo.
"We have reached the final act of the Tour, we've done well, and it went like that in the end. We can be happy, but we were one day short."
Meanwhile, for Porte - who is in the twilight of his career - a podium finish at this year's showpiece event capped off a "dream".
"It's been many years of disappointment, crashes and whatever, dramas," Porte said.
“This is my dream to be on the podium.
"I'm just over the moon it feels like a victory to me to be third.
"Now I can retire happy, this means everything to me."
Don't miss out on the Porte podium party and Caleb Ewan contesting the sprint victory on the Champs-Élysées, the final stage of the 2020 Tour de France. Watch on SBS and SBS On Demand from 11:30pm (AEST) on Sunday, and the SBS ŠKODA Tour Tracker from 11:35pm (AEST).